Aside

Jacob Arie

Contact Info

Skills

Languages

  • Fluent Dutch (Native language)
  • Fluent English (C2 level)

Programming languages

  • R
  • Python
  • Bash
  • SLURM
  • LaTeX
  • Nextflow
  • Snakemake

Main

Jacob Arie van Diermen

MSc

Experience

PhD candidate

Hubrecht institute, developmental epigenomics (Jop Kind Group)

Utrecht, The Netherlands

2026/03 - 2024/09


As a PhD candidate, I conducted research to better understand the fundamental principles of genome regulation during development. This taught me how to process, analyze and present large amounts of genomics data in HPC environments. Moreover, I developed pipelines for preprocessing multimodal genomics data (sciT-snakemake pipeline) and an Accompanying R-package (LoadSciLooms), both of which aid the lab in its research efforts.

Research assistant

Karolinska Institutet, Clinical Neurosciences (Robert Harris Group)

Solna, Sweden

2024/03 - 2023/07


As a continuation of my work as a research intern, I improved the computational pipeline for evolutionary inference with improved parallelization, data cleaning, documentation and Docker containerization for reproducibility. Additionally, I developed a data dashboard using R shiny to improve exploration of the pipeline results. This allowed me to further improve my Python, R and Bash programming expertise

Teaching assistant

Utrecht university, Department of Biology

Utrecht, The Netherlands

2023/05 - 2023/02


As a teaching assistant for the course Kwantitatieve biologie (B-B1KWBI20), I helped first-year biology students grasp statistical concepts and R programming.

Research intern

Karolinska Institutet, Clinical Neurosciences (Robert Harris Group)

Solna, Sweden

2023/03 - 2022/05


As a research intern, I have created a computational pipeline that uses evolutionary inference to better predict which genes are relevant for the regenerative wound-healing in the African Spiny mice. I gained extensive experience in high performance computing (SLURM), programming (R, Python and Bash) and version control (Git, Github). Additionally, I learned to present and report my findings.

Research intern

Utrecht university, Cell biology, neurobiology and biophysics, Anna Akhmanova Group (Cellular dynamics)

Utrecht, The Netherlands

2022/03 - 2021/01


As a research intern, I studied proteins affecting cellular structure. This taught me extensive lab skills, in addition to planning and presenting experimental results.

Education

Utrecht university, Graduate School of Life Sciences

MSc Molecular and Cellular life sciences (MCLS), specialization Biophysics & Molecular Imaging, Bioinformatics minor profile

Utrecht, The Netherlands

2023 - 2020

Bioinformatics minor profile

  • Thesis: Comparative genomics approach finds DNA-repair and immune-related genes in the regenerative African spiny mouse

Major research project

  • Thesis: Characterization of CSPP1 interaction with microtubules in cells

Utrecht university, Department of Biology

BSc in Biology

Utrecht, The Netherlands

2020 - 2017

graduated with honors (cum laude)

Additional skills

Software skills

N/A

N/A

  • Containerization: Docker, Singularity
  • Workflow management: Snakemake, Nextflow
  • Version control: Git, Github
  • Programming: R, Rstudio, Python, Visual studio code, Bash, Zsh, LaTeX
  • Package management: Conda (miniconda, miniforge)
  • OS: Linux (i.e. Debian, Ubuntu)
  • High performance computing (HPC): SLURM
  • Evolutionary inference: HyPhy (aBSREL, MEME), PAML codeml
  • Image analysis: Fiji/ ImageJ